Week 4 – Bioinformatics Work
Hello everyone,
This week my mentor taught me how to analyze gene expression and clinical data from cbioportal.org. This website is an open-source platform with large cancer genomic datasets. Using METABRIC breast cancer data, I was able to create a spreadsheet with gene expression data for ING4, Cxcl10, Cxcr3, and EGFR and clinical data including relapse free status. I then recreated survival curves for ING4 and Cxcr3 (attached below) in GraphPad Prism.
The graphs I created below are similar to the ones in my mentor’s publication here. As shown in Figure 2, breast cancer patients expressing low levels of ING4 (indicated by the red line) have significantly lower disease-free survival (free of any signs of cancer after their primary treatment) than those expressing high levels of ING4. The graph in Figure 1 unfortunately did not show the same trend as in the publication, with patients expressing high levels of Cxcl10 (blue line) having greater disease-free survival than low Cxcl10 expression. This is likely due to an error from my work on the spreadsheet. I will troubleshoot this in week 4 and update the blog post. I will be working with an ING4-deficient breast cancer cell line to characterize the c-terminal end of the receptor for Cxcl10, Cxcr3.
Next week I will be taking a lab orientation class on Monday and starting hands-on work.
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